Shepard's Secret
by TheWooze19
Summary: John Shepherd: Hero of the galaxy, living legend, and...in love? What is he going to do? Especially when it's not normal love. Shep/Thane and Garrus/OC. Takes place between Mass Effect 2 and 3. Thinking of going into a story that takes place during 3 as well. Depends on the response.
1. Chapter 1

Disclaimer: I don't own Mass Effect 2, but I do own Emma; just not her last name.

* * *

**Shepard's Secret**

Chapter 1

"_I'm Commander Shepard and this is my favorite store on the Citadel._" Commander John Shepard smirked as he heard the lilt of his own voice flow through his ears. Seeing this would make one think he was stuck up, but this is not the case at all. He simply finds the sarcasm quite hilarious, you see, Commander Shepard hates the Citadel. Ever since he'd been there as a child he's hated it. He was never sure why, maybe it was because it seemed so clean and pristine and yet no one knew how dirty and filthy it really was or maybe it was just because it was so corrupt. He wasn't really sure what caused his hatred; all he knew is that it would never change.

Shepard sighed as he continued his walk through the market level of the new Citadel, looking for someone very particular; his companions, Garrus and Thane, were just as alert as he was in finding this person. Shepard looked around carefully, scanning each entity in the area and wondering where his target could be. Suddenly, he heard something unusual.

"John? Johnny? Over here," yelled a female voice. John Shepard whipped around to see who had called to him and his face softened. He had found his target. He walked to the girl with a sort of swing in his step and took her into his arms when he reached her. She hugged back but suddenly pushed him away. "Excuse me, but where the hell have you been?" The girl asked this with a glare on her face, her lips pouting.

"Emma Lydia Shepard! Watch your mouth!" Shepard said half-heartedly.

"Wow, John. Look, I'm not you're little sister anymore. I'm an adult now, an adult who's been waiting for you for an hour and a half," The girl, who we now know is called Emma, snapped back.

"Well, you'll always be little to me and besides it's not like there was nothing to do while you waited." Emma sighed and shrugged.

"Yeah, you're right. It's my own fault. So, what are we waiting for? To the Normandy!" Just as Emma was about to head in the direction of the docking bay, her brother's two companions walked up.

"Oh, Emma, these are two of my crew mates; Garrus and Thane." Emma waved and gave a small nod to Thane but when her eyes rested on Garrus she stared. Shepard raised an eyebrow, wondering why his sister was now a drooling idiot. He snapped his fingers in her face a few times and tapped her on the shoulder but nothing worked. He then got an evil idea and stuck his finger in his mouth. When he pulled it out he stuck in right into Emma's ear. She yelped and growled at him.

"Come on Emma, time to go," Shepard said with a small chuckle. Emma just blushed and followed him, grumbling something about "wet ears" as she followed. Thane followed without a beat but Garrus followed slowly, wanting to know very much why his Commander's sister had been staring at him so intently. Most women, whether human or not, stared at him all the time, because of his scarring, but not in the way she had.

* * *

When the four beings arrived on the Normandy Emma was awestruck. She explored the CIC with wide eyes and tingling palms.

"John, this is all yours?" Emma asked excitedly. John smirked and nodded offering his sister a tour. She eagerly accepted and Shepard began pulling her through the ship. After they explored Shepard's cabin and the CIC they took the elevator down a deck. The first room Shepard immediately went to was Life Support. Emma began to follow him in but was stopped by her brother.

"What's the matter John?" Emma asked, confused.

"I-I need to have a minute alone," was his response. Emma raised an eyebrow at this suspicious request. She wanted to see every nook and cranny of the new Normandy but her big brother was making it pretty hard by making her stay out of Life Support.

"But John-,"

"Emma, please?" Emma looked into her brother's eyes and saw desperation. It worried her because someone as tough and strong as her brother was never desperate and she had to know why. It was Emma's time to show why she shared the last name Shepard. She let her brother enter Life Support on his own but she wasn't going to let him off so easily. For now though, Emma was more interested in exploring.

* * *

A/N: So here's the re-edited version of Chapter 1. I'm doing the same to Chapters 2 and 3 so they shall soon follow.


	2. Chapter 2

Disclaimer: I don't own Mass Effect 2, but I do own Emma; just not her last name.

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**Shepard's Secret**

Chapter 2

Emma slowly looked around the 3rd deck of the SR2 and sighed.

"Well Emma, where to now?" She asked herself.

She started shuffling in the direction of Miranda's office but stopped as she watched a certain Turian make his way to the main battery. Curiosity and butterflies filled her stomach as she watched him. He was gruff but graceful as if he had seen so many painful things but those things made him a better being. She had decided then and there that her mission was to get to know more about this Turian, this Garrus.

Meanwhile John was having a dilemma of his own. He clenched his fists as he debated within his mind.

"Come on John. You can do this. You're a hero for God's sake." Shepard mumbled to himself. He took a deep breath and stepped in front of the door, trying not to flinch at the swish it made when it opened. He braced himself and entered the room.

"Shepard, I've been meaning to speak with you," Thane said without missing a beat. There was no turning back now. John sauntered over, trying to cover his chagrin and sat in the chair across from Thane. Thane continued, eyes still closed and hands still folded, with, "So I am curious Shepherd. How is your sister settling in on the Normandy?"

"She likes it just fine."

"I am glad to hear that. But the real reason I wanted to speak with you is regarding myself."

"Thane, we're friends. You don't have to be afraid to share anything with me."

Thane sighed and nodded, finally opening his eyes. "I understand your species has incidents where the same sex may find one another attractive." At this John's breath hitched in his throat and his heart began to pound in his ears.

"Y-yes. G-go on, please."

"I am also aware of this happening, although not often, in Drell culture."

Before Shepard could stop himself he blurted, "Get on with it, Thane."

Thane cleared his throat, nervousness evident in his breathing. "I feel as though I may be one of those instances and-,"

Just as Thane was about to continue the door swished open again to reveal a red faced Emma. John growled mentally and slammed his head down on the table.

"John-John I need to um…just-just come here."

"Emma-,"

"NOW please!"

John sighed and said, "Thane I'm sorry but it'll have to wait. Being a big brother never ends." Thane nodded and his eyes closed again, hands never unfolded.

When he heard the door swish shut his eyes flew open. He slammed his fists on the table and tears began welling up in his eyes. Thane has been waiting almost a year to tell Shepard how he's felt. He doesn't blame Emma but her interruption couldn't have come at a worse moment. "I will tell Shepard how I feel. I swear it," Thane whispered to himself.

* * *

Emma pulled John along into the elevator, John grumbling the whole way. Emma waited to speak after the doors closed and she pressed the button for John's room.

"Oh, holy hell John!"

"What? Emma what is it? What could possibly be so important that you had to interrupt mine and Thane's very important conversation?" Emma stepped back, slightly afraid and pouted. "Emma I'm sorry. It's just-ugh, never mind…what' wrong?"

"Well I talked to your friend Garrus…"

"Emma, what did you do?"

"Nothing! Well, almost nothing." John glared down at his sister and was about to demand she explain but the elevator had stopped and he was once again being dragged by his sister, this time into his room.

"I reiterate, Emma, 'what did you do?'"

"Well after you went to Thane, I decided to the explore the ship on my own. I saw Garrus walking into the main battery and was curious."

"Yeah, curious about his ass."

"John, seriously, shut up? Just let me finish. Anyway, he got all nervous when I walked in after him but I played it cool. He was telling me all about the weapons systems and the main battery and it was actually really interesting-,"

"Emma, seriously, keep going?" John mocked.

"We kissed!" Emma's hands flew to her mouth. John stared at her with a look on his face that Emma wasn't able to determine.

"Emma, I'm-I'm-,"

"John I'm sorry it just sort of happened. If you're mad at me it was an accident and if you're mad at him please don' beat him up."

"Emma I'm happy for you!"

"R-really?"

"Yes."

Emma sighed in relief and smiled. "Good, because he asked me out on a date." John just laughed and ruffled his little sister's hair. "Ok, so now that that's out of the way. I want to know what you and Thane were doing. It seemed a little tense in there." John gulped and tugged at his collar, his face flushing pink.

"Well, you see, it's a long story…"

* * *

A/N: Wow for being close the two Shepards sure don't know each other very well. I'll work on that.


	3. Chapter 3

Disclaimer: I don't own Mass Effect 2, but I do own Emma; just not her last name.

* * *

**Shepherd's Secret**

Chapter 3

"Well, it's a long story…" John stammered. Emma glared at her big brother. For someone who was known as the savior of the Citadel he sure was a fuss bucket. John noticed Emma's frustration and sighed. He really wanted to tell her. Emma and he had been closer than any other brother and sister anyone had ever seen but he still couldn't bring himself to tell her.

"John, I'm your little sister and I love you. Whatever is going on you know you can tell me." John chewed his finger nails nervously while pacing his room. Emma launched herself off the couch, pinning her brother to the floor in an effort to stop his pacing. She then grabbed his arm and twisted it painfully behind his back. In between John's mumbles of protest Emma growled, "Jonathan Theodore Shepard you will tell me what's going on or so help me I'll-I'll strand you on the Citadel for a week!" John shuddered even within the iron grip of his sister at the thought of having to live on the Citadel for a week and finally came to his senses.

"Emma, I'm-I'm…ugh…I'm gay." Emma stared down at her brother with an unreadable expression on her face. She then gently let him go and slowly went back to her seat on the couch. "Emma, please don't be upset. I'm sorry!" John then began to tear up.

"I knew it!" John looked up, startled.

"Wait, what?"

"Johnny, we're closer than ever. You think I didn't know?"

"So, you're not mad?"

"Are you kidding? I'm so glad you finally decided to come out." John smiled at his sister and pulled her into a big bear hug. The two then began chatting noisily about certain things that had given him away; whether they be things recently or even as children.

* * *

Thane paced the CIC nervously not really knowing what he was doing. Other crew members looked at him strangely but none bothered to see what the matter was. Then, there was the ever-friendly Kelly. Her keen eye for emotions made her suspicious of Thane's actions. She had noticed him acting strange around Shepard lately and, being the nosey person she was, wanted to know what was going on. She decided now was as good a time as ever. She skipped up to the pacing Drell and tapped him on the shoulder.

"I was curious as to how long it would take for you to come over here," Thane stated nonchalantly. The peppy Yeoman's eyes widened.

"How did you-? Oh never mind. I came over to see if you were ok. You've been acting kind of strange and I wanted you to know I'm always free to talk."

"I appreciate that Ms. Chambers. I would like that very much in fact." Kelly grinned at Thane and they walked to the comm. room. Kelly felt strange while she was talking to Thane. She felt as though she were some sort of…fag hag and just as she thought this Thane surprised her.

"I am what you humans call gay…."

Kelly smiled softly and said, "And there's nothing wrong with that. Now tell me, is there something else important that has been bothering you?" Kelly noticed Thane's posture stiffen and his fists clench. Her brows knitted in worry and she put a gentle hand on his. At the feel of her hand his fists relaxed as he let out a long breath.

"Ms. Chambers-,"

"Thane, call me Kelly."

Thane smiled, "Kelly, I think I may be in love with Commander Shepard." Kelly grinned at the Drell excitedly. Thane seemed a little uneasy at her grin but then again he would probably feel uneasy no matter what after what he's just told her.

"Thane, you need to tell him," Kelly pressed.

"I cannot. He may not feel the same and he-he would probably find it disgusting." Kelly shook her head harshly, grabbing Thane by the hand.

"The Commander is not like that. Come on Thane let's go think about what you want to say to him." Thane reluctantly let himself be dragged along by the chipper woman sighing as she did so.

* * *

"Emma, I can't tell you how relieved I am that you're ok with this," John stated happily. Emma raised an eyebrow at him and smirked.

"John, what a stupid thing to say; you should have told me this long ago," Emma responded with a giggle. "Now, you have to tell Thane that you love him." John's eyes widened and he almost fell off the couch.

"Wh-why would you assume I'm in love with Thane?" Emma just rolled her eyes and pulled her brother off the couch, the two setting off to find Thane.

* * *

A/N: So they've finally admitted to other people they're gay and in love. Now they have to admit it to one another. I need to get cracking on this story and make it more interesting. Sorry for those of you who favorited it and it sucks right now. I'm just not sure what direction I want this story to go in. I feel like I should make it a tragedy that has a happy ending but I don't know. Ideas are welcome from anyone and thanks for all the faves and alerts and shit. Ciao!


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